Multiple sequence alignment - TraesCS7B01G015800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G015800 chr7B 100.000 2449 0 0 1 2449 13054141 13051693 0.000000e+00 4523.0
1 TraesCS7B01G015800 chr7B 98.199 1499 27 0 1 1499 204459304 204460802 0.000000e+00 2619.0
2 TraesCS7B01G015800 chr7B 97.778 495 10 1 1565 2059 204460784 204461277 0.000000e+00 852.0
3 TraesCS7B01G015800 chr7B 91.743 218 16 2 2232 2449 748422086 748421871 3.960000e-78 302.0
4 TraesCS7B01G015800 chr7B 94.615 130 6 1 2060 2188 666852888 666853017 1.490000e-47 200.0
5 TraesCS7B01G015800 chr7B 97.333 75 2 0 2060 2134 666892344 666892418 7.110000e-26 128.0
6 TraesCS7B01G015800 chr7B 97.143 35 1 0 2154 2188 666872613 666872647 2.630000e-05 60.2
7 TraesCS7B01G015800 chr7B 97.143 35 1 0 2154 2188 666892422 666892456 2.630000e-05 60.2
8 TraesCS7B01G015800 chr3A 99.272 2061 13 1 1 2059 210126907 210124847 0.000000e+00 3722.0
9 TraesCS7B01G015800 chr3A 94.037 218 12 1 2232 2449 745848229 745848445 1.820000e-86 329.0
10 TraesCS7B01G015800 chr3A 93.023 43 2 1 2187 2229 726083174 726083133 7.310000e-06 62.1
11 TraesCS7B01G015800 chr3B 99.333 1499 10 0 1 1499 689987807 689986309 0.000000e+00 2713.0
12 TraesCS7B01G015800 chr3B 97.787 497 10 1 1563 2059 689986329 689985834 0.000000e+00 856.0
13 TraesCS7B01G015800 chr3B 91.057 123 10 1 2063 2184 6242366 6242244 5.420000e-37 165.0
14 TraesCS7B01G015800 chr3B 100.000 59 0 0 1504 1562 479903667 479903609 2.570000e-20 110.0
15 TraesCS7B01G015800 chr3B 100.000 59 0 0 1504 1562 729209866 729209924 2.570000e-20 110.0
16 TraesCS7B01G015800 chr2A 99.266 1499 11 0 1 1499 682560615 682559117 0.000000e+00 2708.0
17 TraesCS7B01G015800 chr2A 98.464 1497 22 1 1 1497 509973528 509972033 0.000000e+00 2636.0
18 TraesCS7B01G015800 chr2A 98.390 497 6 2 1563 2059 682559137 682558643 0.000000e+00 872.0
19 TraesCS7B01G015800 chr2A 97.586 497 11 1 1563 2059 509972051 509971556 0.000000e+00 850.0
20 TraesCS7B01G015800 chr2A 100.000 59 0 0 1504 1562 28827446 28827388 2.570000e-20 110.0
21 TraesCS7B01G015800 chr1B 98.933 1499 16 0 1 1499 222287286 222285788 0.000000e+00 2680.0
22 TraesCS7B01G015800 chr1B 97.988 497 9 1 1563 2059 222285808 222285313 0.000000e+00 861.0
23 TraesCS7B01G015800 chr1B 100.000 59 0 0 1504 1562 159633597 159633539 2.570000e-20 110.0
24 TraesCS7B01G015800 chr1B 96.875 64 1 1 1500 1563 626243745 626243807 3.330000e-19 106.0
25 TraesCS7B01G015800 chr1D 83.584 664 89 12 841 1496 440874997 440875648 2.690000e-169 604.0
26 TraesCS7B01G015800 chr4D 83.179 648 89 11 857 1496 278289243 278289878 2.110000e-160 575.0
27 TraesCS7B01G015800 chr4D 100.000 29 0 0 2183 2211 221300428 221300456 1.000000e-03 54.7
28 TraesCS7B01G015800 chr1A 82.335 668 97 13 841 1499 537147196 537146541 5.910000e-156 560.0
29 TraesCS7B01G015800 chr5A 90.826 218 13 2 2232 2449 640032198 640031988 3.990000e-73 285.0
30 TraesCS7B01G015800 chr5A 94.231 104 5 1 379 481 460411016 460410913 9.070000e-35 158.0
31 TraesCS7B01G015800 chr5A 100.000 60 0 0 1504 1563 515082014 515081955 7.160000e-21 111.0
32 TraesCS7B01G015800 chr5A 97.297 37 0 1 2198 2233 369975838 369975802 7.310000e-06 62.1
33 TraesCS7B01G015800 chr6A 85.638 188 10 5 2060 2230 286237984 286238171 5.380000e-42 182.0
34 TraesCS7B01G015800 chr6A 92.523 107 7 1 380 485 601004505 601004611 4.220000e-33 152.0
35 TraesCS7B01G015800 chr2B 86.667 165 6 2 2081 2229 310495184 310495348 4.190000e-38 169.0
36 TraesCS7B01G015800 chrUn 91.057 123 10 1 2063 2184 470664450 470664328 5.420000e-37 165.0
37 TraesCS7B01G015800 chrUn 100.000 29 0 0 2183 2211 56926573 56926545 1.000000e-03 54.7
38 TraesCS7B01G015800 chr4A 94.231 104 5 1 379 481 146663888 146663785 9.070000e-35 158.0
39 TraesCS7B01G015800 chr4A 96.825 63 2 0 1504 1566 115566436 115566498 3.330000e-19 106.0
40 TraesCS7B01G015800 chr4A 100.000 29 0 0 2183 2211 389240694 389240722 1.000000e-03 54.7
41 TraesCS7B01G015800 chr6B 100.000 59 0 0 1504 1562 187832433 187832491 2.570000e-20 110.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G015800 chr7B 13051693 13054141 2448 True 4523.0 4523 100.0000 1 2449 1 chr7B.!!$R1 2448
1 TraesCS7B01G015800 chr7B 204459304 204461277 1973 False 1735.5 2619 97.9885 1 2059 2 chr7B.!!$F3 2058
2 TraesCS7B01G015800 chr3A 210124847 210126907 2060 True 3722.0 3722 99.2720 1 2059 1 chr3A.!!$R1 2058
3 TraesCS7B01G015800 chr3B 689985834 689987807 1973 True 1784.5 2713 98.5600 1 2059 2 chr3B.!!$R3 2058
4 TraesCS7B01G015800 chr2A 682558643 682560615 1972 True 1790.0 2708 98.8280 1 2059 2 chr2A.!!$R3 2058
5 TraesCS7B01G015800 chr2A 509971556 509973528 1972 True 1743.0 2636 98.0250 1 2059 2 chr2A.!!$R2 2058
6 TraesCS7B01G015800 chr1B 222285313 222287286 1973 True 1770.5 2680 98.4605 1 2059 2 chr1B.!!$R2 2058
7 TraesCS7B01G015800 chr1D 440874997 440875648 651 False 604.0 604 83.5840 841 1496 1 chr1D.!!$F1 655
8 TraesCS7B01G015800 chr4D 278289243 278289878 635 False 575.0 575 83.1790 857 1496 1 chr4D.!!$F2 639
9 TraesCS7B01G015800 chr1A 537146541 537147196 655 True 560.0 560 82.3350 841 1499 1 chr1A.!!$R1 658

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
31 32 0.106708 GTGAGGACTGTGGTCAGCAA 59.893 55.0 0.0 0.0 44.77 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1524 1537 1.450134 TGCATGTAGCTCCCGCTTG 60.45 57.895 0.0 0.0 46.47 4.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 0.106708 GTGAGGACTGTGGTCAGCAA 59.893 55.000 0.00 0.00 44.77 3.91
650 653 8.956533 ATGCTACAAAGGTTGTTTAAAATGTT 57.043 26.923 0.00 0.00 42.22 2.71
1261 1271 6.636447 CGTCAAAAATGAGCTCAACATTGTAA 59.364 34.615 22.50 8.02 37.89 2.41
1524 1537 4.785453 CTTCCCCAGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
1987 2000 0.241749 CATGCAACACGCTGGACATT 59.758 50.000 0.00 0.00 43.06 2.71
2006 2019 4.637172 ACATTCATGTCTATCCCCTCTGGA 60.637 45.833 0.00 0.00 42.13 3.86
2059 2072 1.682684 TGAGCGGAGGAAGGGAGAC 60.683 63.158 0.00 0.00 0.00 3.36
2060 2073 1.380650 GAGCGGAGGAAGGGAGACT 60.381 63.158 0.00 0.00 0.00 3.24
2061 2074 0.106619 GAGCGGAGGAAGGGAGACTA 60.107 60.000 0.00 0.00 0.00 2.59
2062 2075 0.106419 AGCGGAGGAAGGGAGACTAG 60.106 60.000 0.00 0.00 0.00 2.57
2063 2076 0.396001 GCGGAGGAAGGGAGACTAGT 60.396 60.000 0.00 0.00 0.00 2.57
2064 2077 1.133853 GCGGAGGAAGGGAGACTAGTA 60.134 57.143 0.00 0.00 0.00 1.82
2065 2078 2.853705 CGGAGGAAGGGAGACTAGTAG 58.146 57.143 0.00 0.00 0.00 2.57
2066 2079 2.487625 CGGAGGAAGGGAGACTAGTAGG 60.488 59.091 0.00 0.00 0.00 3.18
2067 2080 2.158430 GGAGGAAGGGAGACTAGTAGGG 60.158 59.091 0.00 0.00 0.00 3.53
2068 2081 1.860906 AGGAAGGGAGACTAGTAGGGG 59.139 57.143 0.00 0.00 0.00 4.79
2069 2082 1.707106 GAAGGGAGACTAGTAGGGGC 58.293 60.000 0.00 0.00 0.00 5.80
2070 2083 0.106116 AAGGGAGACTAGTAGGGGCG 60.106 60.000 0.00 0.00 0.00 6.13
2071 2084 1.531128 GGGAGACTAGTAGGGGCGG 60.531 68.421 0.00 0.00 0.00 6.13
2072 2085 1.531128 GGAGACTAGTAGGGGCGGG 60.531 68.421 0.00 0.00 0.00 6.13
2073 2086 1.531128 GAGACTAGTAGGGGCGGGG 60.531 68.421 0.00 0.00 0.00 5.73
2074 2087 3.232483 GACTAGTAGGGGCGGGGC 61.232 72.222 0.00 0.00 0.00 5.80
2086 2099 4.856801 CGGGGCGGAGGATTGGTG 62.857 72.222 0.00 0.00 0.00 4.17
2088 2101 4.424711 GGGCGGAGGATTGGTGCA 62.425 66.667 0.00 0.00 0.00 4.57
2089 2102 2.124151 GGCGGAGGATTGGTGCAT 60.124 61.111 0.00 0.00 0.00 3.96
2090 2103 2.484062 GGCGGAGGATTGGTGCATG 61.484 63.158 0.00 0.00 0.00 4.06
2091 2104 3.113745 CGGAGGATTGGTGCATGC 58.886 61.111 11.82 11.82 0.00 4.06
2092 2105 1.750018 CGGAGGATTGGTGCATGCA 60.750 57.895 18.46 18.46 0.00 3.96
2093 2106 1.105167 CGGAGGATTGGTGCATGCAT 61.105 55.000 25.64 7.59 0.00 3.96
2094 2107 0.672342 GGAGGATTGGTGCATGCATC 59.328 55.000 25.64 24.97 0.00 3.91
2095 2108 1.688772 GAGGATTGGTGCATGCATCT 58.311 50.000 30.00 12.60 0.00 2.90
2096 2109 2.487805 GGAGGATTGGTGCATGCATCTA 60.488 50.000 30.00 23.92 0.00 1.98
2097 2110 2.812591 GAGGATTGGTGCATGCATCTAG 59.187 50.000 30.00 0.00 0.00 2.43
2098 2111 2.174210 AGGATTGGTGCATGCATCTAGT 59.826 45.455 30.00 16.43 0.00 2.57
2099 2112 3.392285 AGGATTGGTGCATGCATCTAGTA 59.608 43.478 30.00 14.06 0.00 1.82
2100 2113 4.136796 GGATTGGTGCATGCATCTAGTAA 58.863 43.478 30.00 17.13 0.00 2.24
2101 2114 4.023707 GGATTGGTGCATGCATCTAGTAAC 60.024 45.833 30.00 15.25 0.00 2.50
2102 2115 2.549926 TGGTGCATGCATCTAGTAACG 58.450 47.619 30.00 0.00 0.00 3.18
2103 2116 1.867233 GGTGCATGCATCTAGTAACGG 59.133 52.381 25.64 0.00 0.00 4.44
2104 2117 2.483013 GGTGCATGCATCTAGTAACGGA 60.483 50.000 25.64 0.00 0.00 4.69
2105 2118 3.393800 GTGCATGCATCTAGTAACGGAT 58.606 45.455 25.64 0.00 0.00 4.18
2106 2119 3.809832 GTGCATGCATCTAGTAACGGATT 59.190 43.478 25.64 0.00 0.00 3.01
2107 2120 4.273480 GTGCATGCATCTAGTAACGGATTT 59.727 41.667 25.64 0.00 0.00 2.17
2108 2121 5.465390 GTGCATGCATCTAGTAACGGATTTA 59.535 40.000 25.64 0.00 0.00 1.40
2109 2122 5.696270 TGCATGCATCTAGTAACGGATTTAG 59.304 40.000 18.46 0.00 0.00 1.85
2110 2123 5.696724 GCATGCATCTAGTAACGGATTTAGT 59.303 40.000 14.21 0.00 0.00 2.24
2111 2124 6.128795 GCATGCATCTAGTAACGGATTTAGTC 60.129 42.308 14.21 0.00 0.00 2.59
2112 2125 5.839621 TGCATCTAGTAACGGATTTAGTCC 58.160 41.667 0.00 0.00 44.10 3.85
2113 2126 5.221382 TGCATCTAGTAACGGATTTAGTCCC 60.221 44.000 0.00 0.00 44.77 4.46
2123 2136 5.868043 CGGATTTAGTCCCGTTACTTTTT 57.132 39.130 0.00 0.00 44.77 1.94
2145 2158 6.523035 TTTTGCCATGGGATATTACTAGGA 57.477 37.500 15.13 0.00 0.00 2.94
2146 2159 5.762179 TTGCCATGGGATATTACTAGGAG 57.238 43.478 15.13 0.00 0.00 3.69
2147 2160 4.104086 TGCCATGGGATATTACTAGGAGG 58.896 47.826 15.13 0.00 0.00 4.30
2148 2161 3.456277 GCCATGGGATATTACTAGGAGGG 59.544 52.174 15.13 0.00 0.00 4.30
2149 2162 4.040755 CCATGGGATATTACTAGGAGGGG 58.959 52.174 2.85 0.00 0.00 4.79
2150 2163 3.866515 TGGGATATTACTAGGAGGGGG 57.133 52.381 0.00 0.00 0.00 5.40
2164 2177 4.235731 GGGGGCGTGATTAGTTGG 57.764 61.111 0.00 0.00 0.00 3.77
2165 2178 1.301954 GGGGGCGTGATTAGTTGGT 59.698 57.895 0.00 0.00 0.00 3.67
2166 2179 0.323087 GGGGGCGTGATTAGTTGGTT 60.323 55.000 0.00 0.00 0.00 3.67
2167 2180 1.541379 GGGGCGTGATTAGTTGGTTT 58.459 50.000 0.00 0.00 0.00 3.27
2168 2181 1.471287 GGGGCGTGATTAGTTGGTTTC 59.529 52.381 0.00 0.00 0.00 2.78
2169 2182 1.129811 GGGCGTGATTAGTTGGTTTCG 59.870 52.381 0.00 0.00 0.00 3.46
2170 2183 1.465187 GGCGTGATTAGTTGGTTTCGC 60.465 52.381 0.00 0.00 41.32 4.70
2171 2184 1.465187 GCGTGATTAGTTGGTTTCGCC 60.465 52.381 0.00 0.00 37.14 5.54
2172 2185 1.129811 CGTGATTAGTTGGTTTCGCCC 59.870 52.381 0.00 0.00 36.04 6.13
2173 2186 2.156098 GTGATTAGTTGGTTTCGCCCA 58.844 47.619 0.00 0.00 36.04 5.36
2174 2187 2.554893 GTGATTAGTTGGTTTCGCCCAA 59.445 45.455 0.00 0.00 42.16 4.12
2175 2188 2.817258 TGATTAGTTGGTTTCGCCCAAG 59.183 45.455 1.86 0.00 44.92 3.61
2176 2189 1.611519 TTAGTTGGTTTCGCCCAAGG 58.388 50.000 1.86 0.00 44.92 3.61
2177 2190 0.766131 TAGTTGGTTTCGCCCAAGGA 59.234 50.000 1.86 0.00 44.92 3.36
2178 2191 0.537371 AGTTGGTTTCGCCCAAGGAG 60.537 55.000 1.86 0.00 44.92 3.69
2179 2192 1.901464 TTGGTTTCGCCCAAGGAGC 60.901 57.895 0.00 0.00 39.56 4.70
2186 2199 2.124736 GCCCAAGGAGCGTGCATA 60.125 61.111 0.00 0.00 0.00 3.14
2187 2200 2.182842 GCCCAAGGAGCGTGCATAG 61.183 63.158 0.00 0.00 0.00 2.23
2188 2201 1.522092 CCCAAGGAGCGTGCATAGA 59.478 57.895 0.00 0.00 0.00 1.98
2189 2202 0.107703 CCCAAGGAGCGTGCATAGAA 60.108 55.000 0.00 0.00 0.00 2.10
2190 2203 1.475751 CCCAAGGAGCGTGCATAGAAT 60.476 52.381 0.00 0.00 0.00 2.40
2191 2204 2.292267 CCAAGGAGCGTGCATAGAATT 58.708 47.619 0.00 0.00 0.00 2.17
2192 2205 3.466836 CCAAGGAGCGTGCATAGAATTA 58.533 45.455 0.00 0.00 0.00 1.40
2193 2206 3.496130 CCAAGGAGCGTGCATAGAATTAG 59.504 47.826 0.00 0.00 0.00 1.73
2194 2207 2.760374 AGGAGCGTGCATAGAATTAGC 58.240 47.619 0.00 0.00 0.00 3.09
2195 2208 1.457303 GGAGCGTGCATAGAATTAGCG 59.543 52.381 0.00 0.00 0.00 4.26
2196 2209 0.861837 AGCGTGCATAGAATTAGCGC 59.138 50.000 0.00 0.00 43.09 5.92
2197 2210 0.861837 GCGTGCATAGAATTAGCGCT 59.138 50.000 17.26 17.26 40.19 5.92
2198 2211 1.261619 GCGTGCATAGAATTAGCGCTT 59.738 47.619 18.68 0.00 40.19 4.68
2199 2212 2.286418 GCGTGCATAGAATTAGCGCTTT 60.286 45.455 18.68 4.02 40.19 3.51
2200 2213 3.788797 GCGTGCATAGAATTAGCGCTTTT 60.789 43.478 18.68 10.53 40.19 2.27
2201 2214 3.720818 CGTGCATAGAATTAGCGCTTTTG 59.279 43.478 18.68 3.37 36.68 2.44
2202 2215 3.483558 GTGCATAGAATTAGCGCTTTTGC 59.516 43.478 18.68 14.79 43.23 3.68
2220 2233 2.787915 GCTCAGGCGCAGTTTAGC 59.212 61.111 10.83 6.72 0.00 3.09
2228 2241 3.047877 GCAGTTTAGCGCCACCGT 61.048 61.111 2.29 0.00 36.67 4.83
2229 2242 1.738830 GCAGTTTAGCGCCACCGTA 60.739 57.895 2.29 0.00 36.67 4.02
2230 2243 1.293267 GCAGTTTAGCGCCACCGTAA 61.293 55.000 2.29 0.00 36.67 3.18
2231 2244 1.365699 CAGTTTAGCGCCACCGTAAT 58.634 50.000 2.29 0.00 36.67 1.89
2232 2245 2.542597 CAGTTTAGCGCCACCGTAATA 58.457 47.619 2.29 0.00 36.67 0.98
2233 2246 2.931325 CAGTTTAGCGCCACCGTAATAA 59.069 45.455 2.29 0.00 36.67 1.40
2234 2247 2.931969 AGTTTAGCGCCACCGTAATAAC 59.068 45.455 2.29 0.00 36.67 1.89
2235 2248 1.938625 TTAGCGCCACCGTAATAACC 58.061 50.000 2.29 0.00 36.67 2.85
2236 2249 0.104671 TAGCGCCACCGTAATAACCC 59.895 55.000 2.29 0.00 36.67 4.11
2237 2250 1.449956 GCGCCACCGTAATAACCCA 60.450 57.895 0.00 0.00 36.67 4.51
2238 2251 1.433837 GCGCCACCGTAATAACCCAG 61.434 60.000 0.00 0.00 36.67 4.45
2239 2252 0.812412 CGCCACCGTAATAACCCAGG 60.812 60.000 0.00 0.00 0.00 4.45
2240 2253 0.542805 GCCACCGTAATAACCCAGGA 59.457 55.000 0.00 0.00 0.00 3.86
2241 2254 1.142262 GCCACCGTAATAACCCAGGAT 59.858 52.381 0.00 0.00 0.00 3.24
2242 2255 2.846193 CCACCGTAATAACCCAGGATG 58.154 52.381 0.00 0.00 0.00 3.51
2243 2256 2.436542 CCACCGTAATAACCCAGGATGA 59.563 50.000 0.00 0.00 39.69 2.92
2244 2257 3.118186 CCACCGTAATAACCCAGGATGAA 60.118 47.826 0.00 0.00 39.69 2.57
2245 2258 4.127171 CACCGTAATAACCCAGGATGAAG 58.873 47.826 0.00 0.00 39.69 3.02
2246 2259 4.035112 ACCGTAATAACCCAGGATGAAGA 58.965 43.478 0.00 0.00 39.69 2.87
2247 2260 4.472108 ACCGTAATAACCCAGGATGAAGAA 59.528 41.667 0.00 0.00 39.69 2.52
2248 2261 5.132144 ACCGTAATAACCCAGGATGAAGAAT 59.868 40.000 0.00 0.00 39.69 2.40
2249 2262 6.328148 ACCGTAATAACCCAGGATGAAGAATA 59.672 38.462 0.00 0.00 39.69 1.75
2250 2263 7.147444 ACCGTAATAACCCAGGATGAAGAATAA 60.147 37.037 0.00 0.00 39.69 1.40
2251 2264 7.883311 CCGTAATAACCCAGGATGAAGAATAAT 59.117 37.037 0.00 0.00 39.69 1.28
2252 2265 9.284968 CGTAATAACCCAGGATGAAGAATAATT 57.715 33.333 0.00 0.00 39.69 1.40
2259 2272 9.942526 ACCCAGGATGAAGAATAATTTATTTCT 57.057 29.630 3.27 0.68 39.69 2.52
2270 2283 9.579932 AGAATAATTTATTTCTCATCCCAGTCC 57.420 33.333 3.27 0.00 0.00 3.85
2271 2284 9.579932 GAATAATTTATTTCTCATCCCAGTCCT 57.420 33.333 3.27 0.00 0.00 3.85
2272 2285 9.942526 AATAATTTATTTCTCATCCCAGTCCTT 57.057 29.630 0.00 0.00 0.00 3.36
2273 2286 7.888250 AATTTATTTCTCATCCCAGTCCTTC 57.112 36.000 0.00 0.00 0.00 3.46
2274 2287 3.550437 ATTTCTCATCCCAGTCCTTCG 57.450 47.619 0.00 0.00 0.00 3.79
2275 2288 2.231716 TTCTCATCCCAGTCCTTCGA 57.768 50.000 0.00 0.00 0.00 3.71
2276 2289 2.461300 TCTCATCCCAGTCCTTCGAT 57.539 50.000 0.00 0.00 0.00 3.59
2277 2290 2.311463 TCTCATCCCAGTCCTTCGATC 58.689 52.381 0.00 0.00 0.00 3.69
2278 2291 1.000827 CTCATCCCAGTCCTTCGATCG 60.001 57.143 9.36 9.36 0.00 3.69
2279 2292 1.032794 CATCCCAGTCCTTCGATCGA 58.967 55.000 15.15 15.15 0.00 3.59
2280 2293 1.000827 CATCCCAGTCCTTCGATCGAG 60.001 57.143 18.54 12.10 0.00 4.04
2281 2294 1.066587 CCCAGTCCTTCGATCGAGC 59.933 63.158 18.54 9.98 0.00 5.03
2282 2295 1.667154 CCCAGTCCTTCGATCGAGCA 61.667 60.000 18.54 3.39 0.00 4.26
2283 2296 0.173481 CCAGTCCTTCGATCGAGCAA 59.827 55.000 18.54 2.58 0.00 3.91
2284 2297 1.554392 CAGTCCTTCGATCGAGCAAG 58.446 55.000 18.54 12.80 0.00 4.01
2285 2298 1.135257 CAGTCCTTCGATCGAGCAAGT 60.135 52.381 18.54 7.48 0.00 3.16
2286 2299 1.133407 AGTCCTTCGATCGAGCAAGTC 59.867 52.381 18.54 8.39 0.00 3.01
2299 2312 4.822107 CGAGCAAGTCGTAACATTATTGG 58.178 43.478 0.00 0.00 44.20 3.16
2300 2313 4.328983 CGAGCAAGTCGTAACATTATTGGT 59.671 41.667 0.00 0.00 44.20 3.67
2301 2314 5.500290 CGAGCAAGTCGTAACATTATTGGTC 60.500 44.000 0.00 0.00 44.20 4.02
2302 2315 4.328983 AGCAAGTCGTAACATTATTGGTCG 59.671 41.667 0.00 0.00 0.00 4.79
2303 2316 4.493545 GCAAGTCGTAACATTATTGGTCGG 60.494 45.833 0.00 0.00 0.00 4.79
2304 2317 4.724074 AGTCGTAACATTATTGGTCGGA 57.276 40.909 0.00 0.00 0.00 4.55
2305 2318 5.272283 AGTCGTAACATTATTGGTCGGAT 57.728 39.130 0.00 0.00 0.00 4.18
2306 2319 5.287226 AGTCGTAACATTATTGGTCGGATC 58.713 41.667 0.00 0.00 0.00 3.36
2307 2320 4.147653 GTCGTAACATTATTGGTCGGATCG 59.852 45.833 0.00 0.00 0.00 3.69
2308 2321 3.121126 CGTAACATTATTGGTCGGATCGC 60.121 47.826 0.00 0.00 0.00 4.58
2309 2322 2.910688 ACATTATTGGTCGGATCGCT 57.089 45.000 0.00 0.00 0.00 4.93
2310 2323 3.194005 ACATTATTGGTCGGATCGCTT 57.806 42.857 0.00 0.00 0.00 4.68
2311 2324 3.541632 ACATTATTGGTCGGATCGCTTT 58.458 40.909 0.00 0.00 0.00 3.51
2312 2325 3.945285 ACATTATTGGTCGGATCGCTTTT 59.055 39.130 0.00 0.00 0.00 2.27
2313 2326 4.035208 ACATTATTGGTCGGATCGCTTTTC 59.965 41.667 0.00 0.00 0.00 2.29
2314 2327 1.379527 ATTGGTCGGATCGCTTTTCC 58.620 50.000 0.00 0.00 0.00 3.13
2320 2333 3.139029 GGATCGCTTTTCCGTCACT 57.861 52.632 0.00 0.00 0.00 3.41
2321 2334 2.288961 GGATCGCTTTTCCGTCACTA 57.711 50.000 0.00 0.00 0.00 2.74
2322 2335 2.822764 GGATCGCTTTTCCGTCACTAT 58.177 47.619 0.00 0.00 0.00 2.12
2323 2336 2.795470 GGATCGCTTTTCCGTCACTATC 59.205 50.000 0.00 0.00 0.00 2.08
2324 2337 3.444916 GATCGCTTTTCCGTCACTATCA 58.555 45.455 0.00 0.00 0.00 2.15
2325 2338 3.306917 TCGCTTTTCCGTCACTATCAA 57.693 42.857 0.00 0.00 0.00 2.57
2326 2339 3.655486 TCGCTTTTCCGTCACTATCAAA 58.345 40.909 0.00 0.00 0.00 2.69
2327 2340 3.430895 TCGCTTTTCCGTCACTATCAAAC 59.569 43.478 0.00 0.00 0.00 2.93
2328 2341 3.424433 CGCTTTTCCGTCACTATCAAACC 60.424 47.826 0.00 0.00 0.00 3.27
2329 2342 3.751698 GCTTTTCCGTCACTATCAAACCT 59.248 43.478 0.00 0.00 0.00 3.50
2330 2343 4.215613 GCTTTTCCGTCACTATCAAACCTT 59.784 41.667 0.00 0.00 0.00 3.50
2331 2344 5.278315 GCTTTTCCGTCACTATCAAACCTTT 60.278 40.000 0.00 0.00 0.00 3.11
2332 2345 6.702716 TTTTCCGTCACTATCAAACCTTTT 57.297 33.333 0.00 0.00 0.00 2.27
2333 2346 5.934935 TTCCGTCACTATCAAACCTTTTC 57.065 39.130 0.00 0.00 0.00 2.29
2334 2347 4.320870 TCCGTCACTATCAAACCTTTTCC 58.679 43.478 0.00 0.00 0.00 3.13
2335 2348 3.439129 CCGTCACTATCAAACCTTTTCCC 59.561 47.826 0.00 0.00 0.00 3.97
2336 2349 3.439129 CGTCACTATCAAACCTTTTCCCC 59.561 47.826 0.00 0.00 0.00 4.81
2337 2350 4.663334 GTCACTATCAAACCTTTTCCCCT 58.337 43.478 0.00 0.00 0.00 4.79
2338 2351 5.077564 GTCACTATCAAACCTTTTCCCCTT 58.922 41.667 0.00 0.00 0.00 3.95
2339 2352 5.048013 GTCACTATCAAACCTTTTCCCCTTG 60.048 44.000 0.00 0.00 0.00 3.61
2340 2353 3.832490 ACTATCAAACCTTTTCCCCTTGC 59.168 43.478 0.00 0.00 0.00 4.01
2341 2354 1.036707 TCAAACCTTTTCCCCTTGCG 58.963 50.000 0.00 0.00 0.00 4.85
2342 2355 0.599991 CAAACCTTTTCCCCTTGCGC 60.600 55.000 0.00 0.00 0.00 6.09
2343 2356 2.082629 AAACCTTTTCCCCTTGCGCG 62.083 55.000 0.00 0.00 0.00 6.86
2344 2357 2.671619 CCTTTTCCCCTTGCGCGA 60.672 61.111 12.10 0.00 0.00 5.87
2345 2358 2.561373 CTTTTCCCCTTGCGCGAC 59.439 61.111 12.10 0.88 0.00 5.19
2346 2359 1.966451 CTTTTCCCCTTGCGCGACT 60.966 57.895 12.10 0.00 0.00 4.18
2347 2360 2.187599 CTTTTCCCCTTGCGCGACTG 62.188 60.000 12.10 0.00 0.00 3.51
2348 2361 2.951475 TTTTCCCCTTGCGCGACTGT 62.951 55.000 12.10 0.00 0.00 3.55
2349 2362 2.102109 TTTCCCCTTGCGCGACTGTA 62.102 55.000 12.10 0.00 0.00 2.74
2350 2363 2.501223 TTCCCCTTGCGCGACTGTAG 62.501 60.000 12.10 0.00 0.00 2.74
2351 2364 2.261671 CCCTTGCGCGACTGTAGT 59.738 61.111 12.10 0.00 0.00 2.73
2352 2365 1.374252 CCCTTGCGCGACTGTAGTT 60.374 57.895 12.10 0.00 0.00 2.24
2353 2366 0.949105 CCCTTGCGCGACTGTAGTTT 60.949 55.000 12.10 0.00 0.00 2.66
2354 2367 0.865769 CCTTGCGCGACTGTAGTTTT 59.134 50.000 12.10 0.00 0.00 2.43
2355 2368 1.263217 CCTTGCGCGACTGTAGTTTTT 59.737 47.619 12.10 0.00 0.00 1.94
2356 2369 2.560896 CTTGCGCGACTGTAGTTTTTC 58.439 47.619 12.10 0.00 0.00 2.29
2357 2370 1.573026 TGCGCGACTGTAGTTTTTCA 58.427 45.000 12.10 0.00 0.00 2.69
2358 2371 1.259507 TGCGCGACTGTAGTTTTTCAC 59.740 47.619 12.10 0.00 0.00 3.18
2359 2372 1.398071 GCGCGACTGTAGTTTTTCACC 60.398 52.381 12.10 0.00 0.00 4.02
2360 2373 1.193874 CGCGACTGTAGTTTTTCACCC 59.806 52.381 0.00 0.00 0.00 4.61
2361 2374 1.534163 GCGACTGTAGTTTTTCACCCC 59.466 52.381 0.00 0.00 0.00 4.95
2362 2375 2.809299 GCGACTGTAGTTTTTCACCCCT 60.809 50.000 0.00 0.00 0.00 4.79
2363 2376 3.064931 CGACTGTAGTTTTTCACCCCTC 58.935 50.000 0.00 0.00 0.00 4.30
2364 2377 3.409570 GACTGTAGTTTTTCACCCCTCC 58.590 50.000 0.00 0.00 0.00 4.30
2365 2378 2.224450 ACTGTAGTTTTTCACCCCTCCG 60.224 50.000 0.00 0.00 0.00 4.63
2366 2379 2.038033 CTGTAGTTTTTCACCCCTCCGA 59.962 50.000 0.00 0.00 0.00 4.55
2367 2380 2.224354 TGTAGTTTTTCACCCCTCCGAC 60.224 50.000 0.00 0.00 0.00 4.79
2368 2381 0.841289 AGTTTTTCACCCCTCCGACA 59.159 50.000 0.00 0.00 0.00 4.35
2369 2382 1.202770 AGTTTTTCACCCCTCCGACAG 60.203 52.381 0.00 0.00 0.00 3.51
2370 2383 0.109723 TTTTTCACCCCTCCGACAGG 59.890 55.000 0.00 0.00 43.01 4.00
2381 2394 4.210724 CCTCCGACAGGGTAATTTTACA 57.789 45.455 3.12 0.00 38.91 2.41
2382 2395 4.777463 CCTCCGACAGGGTAATTTTACAT 58.223 43.478 3.12 0.00 38.91 2.29
2383 2396 5.190677 CCTCCGACAGGGTAATTTTACATT 58.809 41.667 3.12 0.00 38.91 2.71
2384 2397 5.650703 CCTCCGACAGGGTAATTTTACATTT 59.349 40.000 3.12 0.00 38.91 2.32
2385 2398 6.404293 CCTCCGACAGGGTAATTTTACATTTG 60.404 42.308 3.12 1.21 38.91 2.32
2386 2399 6.005198 TCCGACAGGGTAATTTTACATTTGT 58.995 36.000 3.12 3.90 38.33 2.83
2387 2400 6.072397 TCCGACAGGGTAATTTTACATTTGTG 60.072 38.462 3.12 0.00 38.33 3.33
2388 2401 5.571357 CGACAGGGTAATTTTACATTTGTGC 59.429 40.000 3.12 0.00 35.37 4.57
2389 2402 6.569610 CGACAGGGTAATTTTACATTTGTGCT 60.570 38.462 3.12 0.00 35.37 4.40
2390 2403 7.061566 ACAGGGTAATTTTACATTTGTGCTT 57.938 32.000 3.12 0.00 35.37 3.91
2391 2404 6.928492 ACAGGGTAATTTTACATTTGTGCTTG 59.072 34.615 3.12 0.00 35.37 4.01
2392 2405 5.931724 AGGGTAATTTTACATTTGTGCTTGC 59.068 36.000 3.12 0.00 35.37 4.01
2393 2406 5.121611 GGGTAATTTTACATTTGTGCTTGCC 59.878 40.000 3.12 0.00 35.37 4.52
2394 2407 5.698545 GGTAATTTTACATTTGTGCTTGCCA 59.301 36.000 3.12 0.00 35.37 4.92
2395 2408 5.671742 AATTTTACATTTGTGCTTGCCAC 57.328 34.783 0.00 0.00 44.90 5.01
2396 2409 6.615418 GTAATTTTACATTTGTGCTTGCCACG 60.615 38.462 0.00 0.00 39.11 4.94
2397 2410 8.885557 GTAATTTTACATTTGTGCTTGCCACGT 61.886 37.037 0.00 0.00 39.11 4.49
2403 2416 3.568093 GTGCTTGCCACGTCATTTT 57.432 47.368 0.00 0.00 34.22 1.82
2404 2417 2.697431 GTGCTTGCCACGTCATTTTA 57.303 45.000 0.00 0.00 34.22 1.52
2405 2418 2.315901 GTGCTTGCCACGTCATTTTAC 58.684 47.619 0.00 0.00 34.22 2.01
2406 2419 1.950216 TGCTTGCCACGTCATTTTACA 59.050 42.857 0.00 0.00 0.00 2.41
2407 2420 2.359214 TGCTTGCCACGTCATTTTACAA 59.641 40.909 0.00 0.00 0.00 2.41
2408 2421 3.005261 TGCTTGCCACGTCATTTTACAAT 59.995 39.130 0.00 0.00 0.00 2.71
2409 2422 4.216472 TGCTTGCCACGTCATTTTACAATA 59.784 37.500 0.00 0.00 0.00 1.90
2410 2423 4.557301 GCTTGCCACGTCATTTTACAATAC 59.443 41.667 0.00 0.00 0.00 1.89
2411 2424 5.619086 GCTTGCCACGTCATTTTACAATACT 60.619 40.000 0.00 0.00 0.00 2.12
2412 2425 5.950758 TGCCACGTCATTTTACAATACTT 57.049 34.783 0.00 0.00 0.00 2.24
2413 2426 6.320494 TGCCACGTCATTTTACAATACTTT 57.680 33.333 0.00 0.00 0.00 2.66
2414 2427 6.740110 TGCCACGTCATTTTACAATACTTTT 58.260 32.000 0.00 0.00 0.00 2.27
2415 2428 7.203910 TGCCACGTCATTTTACAATACTTTTT 58.796 30.769 0.00 0.00 0.00 1.94
2435 2448 5.961395 TTTTATAGGAAACAGACGCGATC 57.039 39.130 15.93 6.88 0.00 3.69
2436 2449 4.913335 TTATAGGAAACAGACGCGATCT 57.087 40.909 15.93 9.48 38.66 2.75
2437 2450 2.846039 TAGGAAACAGACGCGATCTC 57.154 50.000 15.93 0.00 34.41 2.75
2438 2451 1.178276 AGGAAACAGACGCGATCTCT 58.822 50.000 15.93 1.38 34.41 3.10
2439 2452 1.133407 AGGAAACAGACGCGATCTCTC 59.867 52.381 15.93 0.00 34.41 3.20
2440 2453 1.551145 GAAACAGACGCGATCTCTCC 58.449 55.000 15.93 0.00 34.41 3.71
2441 2454 0.888619 AAACAGACGCGATCTCTCCA 59.111 50.000 15.93 0.00 34.41 3.86
2442 2455 0.453793 AACAGACGCGATCTCTCCAG 59.546 55.000 15.93 2.44 34.41 3.86
2443 2456 1.358402 CAGACGCGATCTCTCCAGG 59.642 63.158 15.93 0.00 34.41 4.45
2444 2457 1.098129 CAGACGCGATCTCTCCAGGA 61.098 60.000 15.93 0.00 34.41 3.86
2445 2458 0.817634 AGACGCGATCTCTCCAGGAG 60.818 60.000 15.93 10.70 43.12 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 0.320421 ATCAACGTGGTAAGCAGCGT 60.320 50.000 0.00 0.00 39.37 5.07
338 339 1.748879 AATCATCAACGTGCGGGGG 60.749 57.895 0.00 0.00 0.00 5.40
715 718 5.082059 GCGACATTATTCAACACTCACAAG 58.918 41.667 0.00 0.00 0.00 3.16
1224 1234 6.470877 GCTCATTTTTGACGTTGAACTTGTTA 59.529 34.615 0.00 0.00 0.00 2.41
1261 1271 4.827692 TGACCATGATGTAGTAAACGCTT 58.172 39.130 0.00 0.00 0.00 4.68
1524 1537 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2006 2019 4.017867 ACTCTCTCTTACTCCTTGTAGCCT 60.018 45.833 0.00 0.00 32.08 4.58
2069 2082 4.856801 CACCAATCCTCCGCCCCG 62.857 72.222 0.00 0.00 0.00 5.73
2071 2084 3.721370 ATGCACCAATCCTCCGCCC 62.721 63.158 0.00 0.00 0.00 6.13
2072 2085 2.124151 ATGCACCAATCCTCCGCC 60.124 61.111 0.00 0.00 0.00 6.13
2073 2086 3.113745 CATGCACCAATCCTCCGC 58.886 61.111 0.00 0.00 0.00 5.54
2074 2087 1.105167 ATGCATGCACCAATCCTCCG 61.105 55.000 25.37 0.00 0.00 4.63
2075 2088 0.672342 GATGCATGCACCAATCCTCC 59.328 55.000 25.37 0.08 0.00 4.30
2076 2089 1.688772 AGATGCATGCACCAATCCTC 58.311 50.000 25.37 14.85 0.00 3.71
2077 2090 2.174210 ACTAGATGCATGCACCAATCCT 59.826 45.455 25.37 14.77 0.00 3.24
2078 2091 2.579873 ACTAGATGCATGCACCAATCC 58.420 47.619 25.37 8.13 0.00 3.01
2079 2092 4.319046 CGTTACTAGATGCATGCACCAATC 60.319 45.833 25.37 16.83 0.00 2.67
2080 2093 3.561310 CGTTACTAGATGCATGCACCAAT 59.439 43.478 25.37 6.94 0.00 3.16
2081 2094 2.935849 CGTTACTAGATGCATGCACCAA 59.064 45.455 25.37 10.05 0.00 3.67
2082 2095 2.549926 CGTTACTAGATGCATGCACCA 58.450 47.619 25.37 10.06 0.00 4.17
2083 2096 1.867233 CCGTTACTAGATGCATGCACC 59.133 52.381 25.37 15.05 0.00 5.01
2084 2097 2.821546 TCCGTTACTAGATGCATGCAC 58.178 47.619 25.37 16.77 0.00 4.57
2085 2098 3.751479 ATCCGTTACTAGATGCATGCA 57.249 42.857 25.04 25.04 0.00 3.96
2086 2099 5.696724 ACTAAATCCGTTACTAGATGCATGC 59.303 40.000 11.82 11.82 0.00 4.06
2087 2100 6.366332 GGACTAAATCCGTTACTAGATGCATG 59.634 42.308 2.46 0.00 37.88 4.06
2088 2101 6.456501 GGACTAAATCCGTTACTAGATGCAT 58.543 40.000 0.00 0.00 37.88 3.96
2089 2102 5.839621 GGACTAAATCCGTTACTAGATGCA 58.160 41.667 0.00 0.00 37.88 3.96
2121 2134 6.916909 TCCTAGTAATATCCCATGGCAAAAA 58.083 36.000 6.09 0.00 0.00 1.94
2122 2135 6.467194 CCTCCTAGTAATATCCCATGGCAAAA 60.467 42.308 6.09 0.00 0.00 2.44
2123 2136 5.014123 CCTCCTAGTAATATCCCATGGCAAA 59.986 44.000 6.09 0.00 0.00 3.68
2124 2137 4.536090 CCTCCTAGTAATATCCCATGGCAA 59.464 45.833 6.09 0.00 0.00 4.52
2125 2138 4.104086 CCTCCTAGTAATATCCCATGGCA 58.896 47.826 6.09 0.00 0.00 4.92
2126 2139 3.456277 CCCTCCTAGTAATATCCCATGGC 59.544 52.174 6.09 0.00 0.00 4.40
2127 2140 4.040755 CCCCTCCTAGTAATATCCCATGG 58.959 52.174 4.14 4.14 0.00 3.66
2128 2141 4.040755 CCCCCTCCTAGTAATATCCCATG 58.959 52.174 0.00 0.00 0.00 3.66
2129 2142 4.369809 CCCCCTCCTAGTAATATCCCAT 57.630 50.000 0.00 0.00 0.00 4.00
2130 2143 3.866515 CCCCCTCCTAGTAATATCCCA 57.133 52.381 0.00 0.00 0.00 4.37
2147 2160 0.323087 AACCAACTAATCACGCCCCC 60.323 55.000 0.00 0.00 0.00 5.40
2148 2161 1.471287 GAAACCAACTAATCACGCCCC 59.529 52.381 0.00 0.00 0.00 5.80
2149 2162 1.129811 CGAAACCAACTAATCACGCCC 59.870 52.381 0.00 0.00 0.00 6.13
2150 2163 1.465187 GCGAAACCAACTAATCACGCC 60.465 52.381 0.00 0.00 39.13 5.68
2151 2164 1.465187 GGCGAAACCAACTAATCACGC 60.465 52.381 0.00 0.00 43.19 5.34
2152 2165 1.129811 GGGCGAAACCAACTAATCACG 59.870 52.381 0.00 0.00 42.05 4.35
2153 2166 2.156098 TGGGCGAAACCAACTAATCAC 58.844 47.619 0.00 0.00 42.05 3.06
2154 2167 2.570415 TGGGCGAAACCAACTAATCA 57.430 45.000 0.00 0.00 42.05 2.57
2155 2168 2.163613 CCTTGGGCGAAACCAACTAATC 59.836 50.000 2.98 0.00 45.19 1.75
2156 2169 2.167662 CCTTGGGCGAAACCAACTAAT 58.832 47.619 2.98 0.00 45.19 1.73
2157 2170 1.143277 TCCTTGGGCGAAACCAACTAA 59.857 47.619 2.98 0.00 45.19 2.24
2158 2171 0.766131 TCCTTGGGCGAAACCAACTA 59.234 50.000 2.98 0.00 45.19 2.24
2159 2172 0.537371 CTCCTTGGGCGAAACCAACT 60.537 55.000 2.98 0.00 45.19 3.16
2160 2173 1.956802 CTCCTTGGGCGAAACCAAC 59.043 57.895 2.98 0.00 45.19 3.77
2162 2175 2.282180 GCTCCTTGGGCGAAACCA 60.282 61.111 0.00 0.00 42.05 3.67
2169 2182 2.124736 TATGCACGCTCCTTGGGC 60.125 61.111 0.00 0.00 0.00 5.36
2170 2183 0.107703 TTCTATGCACGCTCCTTGGG 60.108 55.000 0.00 0.00 0.00 4.12
2171 2184 1.959042 ATTCTATGCACGCTCCTTGG 58.041 50.000 0.00 0.00 0.00 3.61
2172 2185 3.059325 GCTAATTCTATGCACGCTCCTTG 60.059 47.826 0.00 0.00 0.00 3.61
2173 2186 3.134458 GCTAATTCTATGCACGCTCCTT 58.866 45.455 0.00 0.00 0.00 3.36
2174 2187 2.760374 GCTAATTCTATGCACGCTCCT 58.240 47.619 0.00 0.00 0.00 3.69
2175 2188 1.457303 CGCTAATTCTATGCACGCTCC 59.543 52.381 0.00 0.00 0.00 4.70
2176 2189 1.136502 GCGCTAATTCTATGCACGCTC 60.137 52.381 0.00 0.00 41.50 5.03
2177 2190 0.861837 GCGCTAATTCTATGCACGCT 59.138 50.000 0.00 0.00 41.50 5.07
2178 2191 0.861837 AGCGCTAATTCTATGCACGC 59.138 50.000 8.99 4.59 44.79 5.34
2179 2192 3.592381 AAAGCGCTAATTCTATGCACG 57.408 42.857 12.05 0.00 0.00 5.34
2180 2193 3.483558 GCAAAAGCGCTAATTCTATGCAC 59.516 43.478 12.05 0.00 0.00 4.57
2181 2194 3.694734 GCAAAAGCGCTAATTCTATGCA 58.305 40.909 12.05 0.00 0.00 3.96
2182 2195 2.715997 CGCAAAAGCGCTAATTCTATGC 59.284 45.455 12.05 12.55 0.00 3.14
2203 2216 2.787915 GCTAAACTGCGCCTGAGC 59.212 61.111 4.18 2.75 37.71 4.26
2211 2224 1.293267 TTACGGTGGCGCTAAACTGC 61.293 55.000 7.64 0.00 0.00 4.40
2212 2225 1.365699 ATTACGGTGGCGCTAAACTG 58.634 50.000 7.64 11.35 0.00 3.16
2213 2226 2.931969 GTTATTACGGTGGCGCTAAACT 59.068 45.455 7.64 0.00 0.00 2.66
2214 2227 2.030823 GGTTATTACGGTGGCGCTAAAC 59.969 50.000 7.64 3.38 0.00 2.01
2215 2228 2.278854 GGTTATTACGGTGGCGCTAAA 58.721 47.619 7.64 0.00 0.00 1.85
2216 2229 1.473080 GGGTTATTACGGTGGCGCTAA 60.473 52.381 7.64 0.00 0.00 3.09
2217 2230 0.104671 GGGTTATTACGGTGGCGCTA 59.895 55.000 7.64 0.00 0.00 4.26
2218 2231 1.153309 GGGTTATTACGGTGGCGCT 60.153 57.895 7.64 0.00 0.00 5.92
2219 2232 1.433837 CTGGGTTATTACGGTGGCGC 61.434 60.000 0.00 0.00 0.00 6.53
2220 2233 0.812412 CCTGGGTTATTACGGTGGCG 60.812 60.000 0.00 0.00 0.00 5.69
2221 2234 0.542805 TCCTGGGTTATTACGGTGGC 59.457 55.000 0.00 0.00 0.00 5.01
2222 2235 2.436542 TCATCCTGGGTTATTACGGTGG 59.563 50.000 0.00 0.00 0.00 4.61
2223 2236 3.830744 TCATCCTGGGTTATTACGGTG 57.169 47.619 0.00 0.00 0.00 4.94
2224 2237 4.035112 TCTTCATCCTGGGTTATTACGGT 58.965 43.478 0.00 0.00 0.00 4.83
2225 2238 4.682778 TCTTCATCCTGGGTTATTACGG 57.317 45.455 0.00 0.00 0.00 4.02
2226 2239 8.848474 ATTATTCTTCATCCTGGGTTATTACG 57.152 34.615 0.00 0.00 0.00 3.18
2233 2246 9.942526 AGAAATAAATTATTCTTCATCCTGGGT 57.057 29.630 0.00 0.00 32.05 4.51
2244 2257 9.579932 GGACTGGGATGAGAAATAAATTATTCT 57.420 33.333 0.00 1.85 38.56 2.40
2245 2258 9.579932 AGGACTGGGATGAGAAATAAATTATTC 57.420 33.333 0.00 0.00 0.00 1.75
2246 2259 9.942526 AAGGACTGGGATGAGAAATAAATTATT 57.057 29.630 0.00 0.00 0.00 1.40
2247 2260 9.579932 GAAGGACTGGGATGAGAAATAAATTAT 57.420 33.333 0.00 0.00 0.00 1.28
2248 2261 7.715249 CGAAGGACTGGGATGAGAAATAAATTA 59.285 37.037 0.00 0.00 0.00 1.40
2249 2262 6.543831 CGAAGGACTGGGATGAGAAATAAATT 59.456 38.462 0.00 0.00 0.00 1.82
2250 2263 6.058183 CGAAGGACTGGGATGAGAAATAAAT 58.942 40.000 0.00 0.00 0.00 1.40
2251 2264 5.188948 TCGAAGGACTGGGATGAGAAATAAA 59.811 40.000 0.00 0.00 0.00 1.40
2252 2265 4.714802 TCGAAGGACTGGGATGAGAAATAA 59.285 41.667 0.00 0.00 0.00 1.40
2253 2266 4.286707 TCGAAGGACTGGGATGAGAAATA 58.713 43.478 0.00 0.00 0.00 1.40
2254 2267 3.107601 TCGAAGGACTGGGATGAGAAAT 58.892 45.455 0.00 0.00 0.00 2.17
2255 2268 2.536066 TCGAAGGACTGGGATGAGAAA 58.464 47.619 0.00 0.00 0.00 2.52
2256 2269 2.231716 TCGAAGGACTGGGATGAGAA 57.768 50.000 0.00 0.00 0.00 2.87
2257 2270 2.311463 GATCGAAGGACTGGGATGAGA 58.689 52.381 0.00 0.00 0.00 3.27
2258 2271 1.000827 CGATCGAAGGACTGGGATGAG 60.001 57.143 10.26 0.00 0.00 2.90
2259 2272 1.032794 CGATCGAAGGACTGGGATGA 58.967 55.000 10.26 0.00 0.00 2.92
2260 2273 1.000827 CTCGATCGAAGGACTGGGATG 60.001 57.143 19.92 0.00 0.00 3.51
2261 2274 1.323412 CTCGATCGAAGGACTGGGAT 58.677 55.000 19.92 0.00 0.00 3.85
2262 2275 1.384989 GCTCGATCGAAGGACTGGGA 61.385 60.000 19.92 0.00 0.00 4.37
2263 2276 1.066587 GCTCGATCGAAGGACTGGG 59.933 63.158 19.92 5.82 0.00 4.45
2264 2277 0.173481 TTGCTCGATCGAAGGACTGG 59.827 55.000 19.92 6.59 0.00 4.00
2265 2278 1.135257 ACTTGCTCGATCGAAGGACTG 60.135 52.381 19.92 7.35 0.00 3.51
2266 2279 1.133407 GACTTGCTCGATCGAAGGACT 59.867 52.381 19.92 1.55 0.00 3.85
2267 2280 1.551145 GACTTGCTCGATCGAAGGAC 58.449 55.000 19.92 9.44 0.00 3.85
2268 2281 0.098905 CGACTTGCTCGATCGAAGGA 59.901 55.000 19.92 11.52 46.14 3.36
2269 2282 0.179161 ACGACTTGCTCGATCGAAGG 60.179 55.000 19.92 9.65 46.14 3.46
2270 2283 2.453650 TACGACTTGCTCGATCGAAG 57.546 50.000 19.92 15.85 46.14 3.79
2271 2284 2.095617 TGTTACGACTTGCTCGATCGAA 60.096 45.455 19.92 1.73 46.14 3.71
2272 2285 1.465777 TGTTACGACTTGCTCGATCGA 59.534 47.619 18.32 18.32 46.14 3.59
2273 2286 1.891178 TGTTACGACTTGCTCGATCG 58.109 50.000 9.36 9.36 46.14 3.69
2274 2287 6.347881 CAATAATGTTACGACTTGCTCGATC 58.652 40.000 0.37 0.00 46.14 3.69
2275 2288 5.234329 CCAATAATGTTACGACTTGCTCGAT 59.766 40.000 0.37 0.00 46.14 3.59
2276 2289 4.565166 CCAATAATGTTACGACTTGCTCGA 59.435 41.667 0.37 0.00 46.14 4.04
2278 2291 5.500290 CGACCAATAATGTTACGACTTGCTC 60.500 44.000 0.00 0.00 0.00 4.26
2279 2292 4.328983 CGACCAATAATGTTACGACTTGCT 59.671 41.667 0.00 0.00 0.00 3.91
2280 2293 4.493545 CCGACCAATAATGTTACGACTTGC 60.494 45.833 0.00 0.00 0.00 4.01
2281 2294 4.865925 TCCGACCAATAATGTTACGACTTG 59.134 41.667 0.00 0.00 0.00 3.16
2282 2295 5.075858 TCCGACCAATAATGTTACGACTT 57.924 39.130 0.00 0.00 0.00 3.01
2283 2296 4.724074 TCCGACCAATAATGTTACGACT 57.276 40.909 0.00 0.00 0.00 4.18
2284 2297 4.147653 CGATCCGACCAATAATGTTACGAC 59.852 45.833 0.00 0.00 0.00 4.34
2285 2298 4.292599 CGATCCGACCAATAATGTTACGA 58.707 43.478 0.00 0.00 0.00 3.43
2286 2299 3.121126 GCGATCCGACCAATAATGTTACG 60.121 47.826 0.00 0.00 0.00 3.18
2287 2300 4.056050 AGCGATCCGACCAATAATGTTAC 58.944 43.478 0.00 0.00 0.00 2.50
2288 2301 4.330944 AGCGATCCGACCAATAATGTTA 57.669 40.909 0.00 0.00 0.00 2.41
2289 2302 3.194005 AGCGATCCGACCAATAATGTT 57.806 42.857 0.00 0.00 0.00 2.71
2290 2303 2.910688 AGCGATCCGACCAATAATGT 57.089 45.000 0.00 0.00 0.00 2.71
2291 2304 4.527564 GAAAAGCGATCCGACCAATAATG 58.472 43.478 0.00 0.00 0.00 1.90
2292 2305 3.564225 GGAAAAGCGATCCGACCAATAAT 59.436 43.478 0.00 0.00 0.00 1.28
2293 2306 2.940410 GGAAAAGCGATCCGACCAATAA 59.060 45.455 0.00 0.00 0.00 1.40
2294 2307 2.557317 GGAAAAGCGATCCGACCAATA 58.443 47.619 0.00 0.00 0.00 1.90
2295 2308 1.379527 GGAAAAGCGATCCGACCAAT 58.620 50.000 0.00 0.00 0.00 3.16
2296 2309 2.849081 GGAAAAGCGATCCGACCAA 58.151 52.632 0.00 0.00 0.00 3.67
2297 2310 4.609995 GGAAAAGCGATCCGACCA 57.390 55.556 0.00 0.00 0.00 4.02
2302 2315 2.288961 TAGTGACGGAAAAGCGATCC 57.711 50.000 0.00 0.00 0.00 3.36
2303 2316 3.444916 TGATAGTGACGGAAAAGCGATC 58.555 45.455 0.00 0.00 0.00 3.69
2304 2317 3.520290 TGATAGTGACGGAAAAGCGAT 57.480 42.857 0.00 0.00 0.00 4.58
2305 2318 3.306917 TTGATAGTGACGGAAAAGCGA 57.693 42.857 0.00 0.00 0.00 4.93
2306 2319 3.424433 GGTTTGATAGTGACGGAAAAGCG 60.424 47.826 0.00 0.00 0.00 4.68
2307 2320 3.751698 AGGTTTGATAGTGACGGAAAAGC 59.248 43.478 0.00 0.00 0.00 3.51
2308 2321 5.941948 AAGGTTTGATAGTGACGGAAAAG 57.058 39.130 0.00 0.00 0.00 2.27
2309 2322 6.238814 GGAAAAGGTTTGATAGTGACGGAAAA 60.239 38.462 0.00 0.00 0.00 2.29
2310 2323 5.239963 GGAAAAGGTTTGATAGTGACGGAAA 59.760 40.000 0.00 0.00 0.00 3.13
2311 2324 4.758165 GGAAAAGGTTTGATAGTGACGGAA 59.242 41.667 0.00 0.00 0.00 4.30
2312 2325 4.320870 GGAAAAGGTTTGATAGTGACGGA 58.679 43.478 0.00 0.00 0.00 4.69
2313 2326 3.439129 GGGAAAAGGTTTGATAGTGACGG 59.561 47.826 0.00 0.00 0.00 4.79
2314 2327 3.439129 GGGGAAAAGGTTTGATAGTGACG 59.561 47.826 0.00 0.00 0.00 4.35
2315 2328 4.663334 AGGGGAAAAGGTTTGATAGTGAC 58.337 43.478 0.00 0.00 0.00 3.67
2316 2329 5.076873 CAAGGGGAAAAGGTTTGATAGTGA 58.923 41.667 0.00 0.00 0.00 3.41
2317 2330 4.321974 GCAAGGGGAAAAGGTTTGATAGTG 60.322 45.833 0.00 0.00 0.00 2.74
2318 2331 3.832490 GCAAGGGGAAAAGGTTTGATAGT 59.168 43.478 0.00 0.00 0.00 2.12
2319 2332 3.119495 CGCAAGGGGAAAAGGTTTGATAG 60.119 47.826 0.00 0.00 0.00 2.08
2320 2333 2.823154 CGCAAGGGGAAAAGGTTTGATA 59.177 45.455 0.00 0.00 0.00 2.15
2321 2334 1.618343 CGCAAGGGGAAAAGGTTTGAT 59.382 47.619 0.00 0.00 0.00 2.57
2322 2335 1.036707 CGCAAGGGGAAAAGGTTTGA 58.963 50.000 0.00 0.00 0.00 2.69
2323 2336 0.599991 GCGCAAGGGGAAAAGGTTTG 60.600 55.000 0.30 0.00 38.28 2.93
2324 2337 1.745890 GCGCAAGGGGAAAAGGTTT 59.254 52.632 0.30 0.00 38.28 3.27
2325 2338 3.455152 GCGCAAGGGGAAAAGGTT 58.545 55.556 0.30 0.00 38.28 3.50
2335 2348 0.865769 AAAACTACAGTCGCGCAAGG 59.134 50.000 8.75 0.00 38.28 3.61
2336 2349 2.033236 TGAAAAACTACAGTCGCGCAAG 60.033 45.455 8.75 0.00 43.44 4.01
2337 2350 1.934525 TGAAAAACTACAGTCGCGCAA 59.065 42.857 8.75 0.00 0.00 4.85
2338 2351 1.259507 GTGAAAAACTACAGTCGCGCA 59.740 47.619 8.75 0.00 0.00 6.09
2339 2352 1.398071 GGTGAAAAACTACAGTCGCGC 60.398 52.381 0.00 0.00 0.00 6.86
2340 2353 1.193874 GGGTGAAAAACTACAGTCGCG 59.806 52.381 0.00 0.00 0.00 5.87
2341 2354 1.534163 GGGGTGAAAAACTACAGTCGC 59.466 52.381 0.00 0.00 0.00 5.19
2342 2355 3.064931 GAGGGGTGAAAAACTACAGTCG 58.935 50.000 0.00 0.00 0.00 4.18
2343 2356 3.409570 GGAGGGGTGAAAAACTACAGTC 58.590 50.000 0.00 0.00 0.00 3.51
2344 2357 2.224450 CGGAGGGGTGAAAAACTACAGT 60.224 50.000 0.00 0.00 0.00 3.55
2345 2358 2.038033 TCGGAGGGGTGAAAAACTACAG 59.962 50.000 0.00 0.00 0.00 2.74
2346 2359 2.048601 TCGGAGGGGTGAAAAACTACA 58.951 47.619 0.00 0.00 0.00 2.74
2347 2360 2.224354 TGTCGGAGGGGTGAAAAACTAC 60.224 50.000 0.00 0.00 0.00 2.73
2348 2361 2.038033 CTGTCGGAGGGGTGAAAAACTA 59.962 50.000 0.00 0.00 0.00 2.24
2349 2362 0.841289 TGTCGGAGGGGTGAAAAACT 59.159 50.000 0.00 0.00 0.00 2.66
2350 2363 1.235724 CTGTCGGAGGGGTGAAAAAC 58.764 55.000 0.00 0.00 0.00 2.43
2351 2364 0.109723 CCTGTCGGAGGGGTGAAAAA 59.890 55.000 0.00 0.00 38.36 1.94
2352 2365 1.758592 CCTGTCGGAGGGGTGAAAA 59.241 57.895 0.00 0.00 38.36 2.29
2353 2366 3.478780 CCTGTCGGAGGGGTGAAA 58.521 61.111 0.00 0.00 38.36 2.69
2360 2373 4.210724 TGTAAAATTACCCTGTCGGAGG 57.789 45.455 1.13 0.00 42.38 4.30
2361 2374 6.150474 ACAAATGTAAAATTACCCTGTCGGAG 59.850 38.462 1.13 0.00 34.64 4.63
2362 2375 6.005198 ACAAATGTAAAATTACCCTGTCGGA 58.995 36.000 1.13 0.00 34.64 4.55
2363 2376 6.090129 CACAAATGTAAAATTACCCTGTCGG 58.910 40.000 1.13 0.00 32.72 4.79
2364 2377 5.571357 GCACAAATGTAAAATTACCCTGTCG 59.429 40.000 1.13 0.00 32.72 4.35
2365 2378 6.687604 AGCACAAATGTAAAATTACCCTGTC 58.312 36.000 1.13 0.00 32.72 3.51
2366 2379 6.664428 AGCACAAATGTAAAATTACCCTGT 57.336 33.333 1.13 0.10 32.72 4.00
2367 2380 6.128580 GCAAGCACAAATGTAAAATTACCCTG 60.129 38.462 1.13 0.00 32.72 4.45
2368 2381 5.931724 GCAAGCACAAATGTAAAATTACCCT 59.068 36.000 1.13 0.00 32.72 4.34
2369 2382 5.121611 GGCAAGCACAAATGTAAAATTACCC 59.878 40.000 1.13 0.00 32.72 3.69
2370 2383 5.698545 TGGCAAGCACAAATGTAAAATTACC 59.301 36.000 1.13 0.00 32.72 2.85
2371 2384 6.589454 GTGGCAAGCACAAATGTAAAATTAC 58.411 36.000 0.00 0.00 0.00 1.89
2372 2385 5.403766 CGTGGCAAGCACAAATGTAAAATTA 59.596 36.000 0.00 0.00 0.00 1.40
2373 2386 4.210955 CGTGGCAAGCACAAATGTAAAATT 59.789 37.500 0.00 0.00 0.00 1.82
2374 2387 3.740321 CGTGGCAAGCACAAATGTAAAAT 59.260 39.130 0.00 0.00 0.00 1.82
2375 2388 3.119291 CGTGGCAAGCACAAATGTAAAA 58.881 40.909 0.00 0.00 0.00 1.52
2376 2389 2.099921 ACGTGGCAAGCACAAATGTAAA 59.900 40.909 0.00 0.00 0.00 2.01
2377 2390 1.678627 ACGTGGCAAGCACAAATGTAA 59.321 42.857 0.00 0.00 0.00 2.41
2378 2391 1.265635 GACGTGGCAAGCACAAATGTA 59.734 47.619 0.00 0.00 0.00 2.29
2379 2392 0.030638 GACGTGGCAAGCACAAATGT 59.969 50.000 0.00 0.00 0.00 2.71
2380 2393 0.030504 TGACGTGGCAAGCACAAATG 59.969 50.000 0.00 0.00 0.00 2.32
2381 2394 0.961019 ATGACGTGGCAAGCACAAAT 59.039 45.000 0.00 0.00 0.00 2.32
2382 2395 0.743688 AATGACGTGGCAAGCACAAA 59.256 45.000 0.00 0.00 0.00 2.83
2383 2396 0.743688 AAATGACGTGGCAAGCACAA 59.256 45.000 0.00 0.00 0.00 3.33
2384 2397 0.743688 AAAATGACGTGGCAAGCACA 59.256 45.000 0.00 1.85 0.00 4.57
2385 2398 2.287308 TGTAAAATGACGTGGCAAGCAC 60.287 45.455 0.00 0.00 0.00 4.40
2386 2399 1.950216 TGTAAAATGACGTGGCAAGCA 59.050 42.857 0.00 0.07 0.00 3.91
2387 2400 2.697431 TGTAAAATGACGTGGCAAGC 57.303 45.000 0.00 0.00 0.00 4.01
2388 2401 5.938322 AGTATTGTAAAATGACGTGGCAAG 58.062 37.500 0.00 0.00 0.00 4.01
2389 2402 5.950758 AGTATTGTAAAATGACGTGGCAA 57.049 34.783 0.00 0.00 0.00 4.52
2390 2403 5.950758 AAGTATTGTAAAATGACGTGGCA 57.049 34.783 0.00 0.00 0.00 4.92
2391 2404 7.631915 AAAAAGTATTGTAAAATGACGTGGC 57.368 32.000 0.00 0.00 0.00 5.01
2412 2425 6.103997 AGATCGCGTCTGTTTCCTATAAAAA 58.896 36.000 5.77 0.00 35.31 1.94
2413 2426 5.657474 AGATCGCGTCTGTTTCCTATAAAA 58.343 37.500 5.77 0.00 35.31 1.52
2414 2427 5.067413 AGAGATCGCGTCTGTTTCCTATAAA 59.933 40.000 14.47 0.00 37.29 1.40
2415 2428 4.579340 AGAGATCGCGTCTGTTTCCTATAA 59.421 41.667 14.47 0.00 37.29 0.98
2416 2429 4.135306 AGAGATCGCGTCTGTTTCCTATA 58.865 43.478 14.47 0.00 37.29 1.31
2417 2430 2.952978 AGAGATCGCGTCTGTTTCCTAT 59.047 45.455 14.47 0.00 37.29 2.57
2418 2431 2.355132 GAGAGATCGCGTCTGTTTCCTA 59.645 50.000 14.47 0.00 37.29 2.94
2419 2432 1.133407 GAGAGATCGCGTCTGTTTCCT 59.867 52.381 14.47 6.33 37.29 3.36
2420 2433 1.551145 GAGAGATCGCGTCTGTTTCC 58.449 55.000 14.47 2.21 37.29 3.13
2421 2434 1.135373 TGGAGAGATCGCGTCTGTTTC 60.135 52.381 14.47 9.59 37.29 2.78
2422 2435 0.888619 TGGAGAGATCGCGTCTGTTT 59.111 50.000 14.47 2.46 37.29 2.83
2423 2436 0.453793 CTGGAGAGATCGCGTCTGTT 59.546 55.000 14.47 4.54 37.29 3.16
2424 2437 1.380403 CCTGGAGAGATCGCGTCTGT 61.380 60.000 14.47 11.10 37.29 3.41
2425 2438 1.098129 TCCTGGAGAGATCGCGTCTG 61.098 60.000 14.47 2.16 37.29 3.51
2426 2439 0.817634 CTCCTGGAGAGATCGCGTCT 60.818 60.000 19.13 8.58 46.50 4.18
2427 2440 1.652012 CTCCTGGAGAGATCGCGTC 59.348 63.158 19.13 2.98 46.50 5.19
2428 2441 3.834726 CTCCTGGAGAGATCGCGT 58.165 61.111 19.13 0.00 46.50 6.01


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.